jalview.git
17 years agomoved dataset sequence creation onto sequence method
jprocter [Thu, 30 Aug 2007 11:40:34 +0000 (11:40 +0000)]
moved dataset sequence creation onto sequence method

17 years agocreate dataset sequence method
jprocter [Thu, 30 Aug 2007 11:40:09 +0000 (11:40 +0000)]
create dataset sequence method

17 years agoremoved autogenerated todo
jprocter [Thu, 30 Aug 2007 11:39:46 +0000 (11:39 +0000)]
removed autogenerated todo

17 years agoupdated source generation for castor-1.1-cycle patched
jprocter [Thu, 30 Aug 2007 11:39:02 +0000 (11:39 +0000)]
updated source generation for castor-1.1-cycle patched

17 years agoadded aligned codon frames, and dataset reference ids for sequenceSet and sequences...
jprocter [Thu, 30 Aug 2007 11:38:08 +0000 (11:38 +0000)]
added aligned codon frames, and dataset reference ids for sequenceSet and sequences to project xml

17 years agoapplet and application menu entry differences and consensus only differences
jprocter [Wed, 29 Aug 2007 12:39:25 +0000 (12:39 +0000)]
applet and application menu entry differences and consensus only differences

17 years agodataset alignments have a reference count which must be zero before they are finalized.
jprocter [Fri, 24 Aug 2007 15:38:29 +0000 (15:38 +0000)]
dataset alignments have a reference count which must be zero before they are finalized.

17 years agoremove null pointer exception when embl file is not retrieved and comment about selec...
jprocter [Fri, 24 Aug 2007 15:37:12 +0000 (15:37 +0000)]
remove null pointer exception when embl file is not retrieved and comment about selecting for peptide or na sequences

17 years agotodo comments
jprocter [Fri, 24 Aug 2007 15:20:33 +0000 (15:20 +0000)]
todo comments

17 years agoproper vamsas style binding of alignment sequence objects to newick node labels....
jprocter [Thu, 23 Aug 2007 11:52:32 +0000 (11:52 +0000)]
proper vamsas style binding of alignment sequence objects to newick node labels. modified binding of vamsas alignment to the SequenceSet id from the alignment viewport.

17 years agoslightly faster validation patch (logging message concatenation and IdentityHashset...
jprocter [Thu, 23 Aug 2007 11:49:53 +0000 (11:49 +0000)]
slightly faster validation patch (logging message concatenation and IdentityHashset patch to 1.1-cycle source)

17 years agobugfixed and removed some inefficiencies in marshalling
jprocter [Thu, 23 Aug 2007 11:48:53 +0000 (11:48 +0000)]
bugfixed and removed some inefficiencies in marshalling

17 years agopopup for non-fatal tree parsing error
jprocter [Wed, 22 Aug 2007 13:44:37 +0000 (13:44 +0000)]
popup for non-fatal tree parsing error

17 years agoquick fix for exceptions due to invalid embl refs
jprocter [Wed, 22 Aug 2007 13:43:28 +0000 (13:43 +0000)]
quick fix for exceptions due to invalid embl refs

17 years agofix serious repetitive exceptions if user closes colour dialog box without selecting...
jprocter [Wed, 22 Aug 2007 13:32:51 +0000 (13:32 +0000)]
fix serious repetitive exceptions if user closes colour dialog box without selecting colour

17 years agocatch occasional -ve imgWidth exception
jprocter [Wed, 22 Aug 2007 13:31:38 +0000 (13:31 +0000)]
catch occasional -ve imgWidth exception

17 years agoadded failsafe fix for cases where null sequence names are passed to constructor
jprocter [Wed, 22 Aug 2007 13:31:02 +0000 (13:31 +0000)]
added failsafe fix for cases where null sequence names are passed to constructor

17 years agointroduce beginning of bug fix for parsing atv style newick tree files where the...
jprocter [Wed, 22 Aug 2007 13:28:02 +0000 (13:28 +0000)]
introduce beginning of bug fix for parsing atv style newick tree files where the NHX comment appears between the node info (label bootstrap:distance[nhx&...]). Comments now raise a non-fatal warning message about incorrect tree parsing.

17 years agoadded facility for sending non-fatal warnings back to caller.
jprocter [Wed, 22 Aug 2007 13:26:25 +0000 (13:26 +0000)]
added facility for sending non-fatal warnings back to caller.

17 years agofixed typo in new 2_3 startup file default value
jprocter [Mon, 13 Aug 2007 09:49:55 +0000 (09:49 +0000)]
fixed typo in new 2_3 startup file default value

17 years agogive treeviewer description its own contents entry and link it in better.
jprocter [Wed, 8 Aug 2007 11:59:20 +0000 (11:59 +0000)]
give treeviewer description its own contents entry and link it in better.

17 years agogeneralise name of prediction method
jprocter [Wed, 8 Aug 2007 11:58:49 +0000 (11:58 +0000)]
generalise name of prediction method

17 years agoensure default source dist is relative to basedir of build
jprocter [Wed, 8 Aug 2007 09:46:23 +0000 (09:46 +0000)]
ensure default source dist is relative to basedir of build

17 years agoallow source dist archive to be an absolute filename
jprocter [Wed, 8 Aug 2007 09:45:36 +0000 (09:45 +0000)]
allow source dist archive to be an absolute filename

17 years agoadded source-dist task
jprocter [Wed, 8 Aug 2007 09:32:00 +0000 (09:32 +0000)]
added source-dist task

17 years agohistidine should be midblue (noticed by Peter Knight via jalview-help)
jprocter [Wed, 8 Aug 2007 08:07:39 +0000 (08:07 +0000)]
histidine should be midblue (noticed by Peter Knight via jalview-help)

17 years agocomment concerning null exceptions generated when annotations read from a file are...
jprocter [Mon, 6 Aug 2007 14:40:34 +0000 (14:40 +0000)]
comment concerning null exceptions generated when annotations read from a file are rendered in the applet

17 years agonull pointer exception blocked redraw of annotation added to alignment via applet...
jprocter [Mon, 6 Aug 2007 14:25:29 +0000 (14:25 +0000)]
null pointer exception blocked redraw of annotation added to alignment via applet's annotations parameter

17 years agojavadoc and bugfix for 'save' when jalview is default format
jprocter [Thu, 2 Aug 2007 10:16:46 +0000 (10:16 +0000)]
javadoc and bugfix for 'save' when jalview is default format

17 years agoupdated vamsas library (version for iscb demo)
jprocter [Thu, 2 Aug 2007 10:16:13 +0000 (10:16 +0000)]
updated vamsas library (version for iscb demo)

17 years agoignore contents of this directory
jprocter [Wed, 1 Aug 2007 16:50:29 +0000 (16:50 +0000)]
ignore contents of this directory

17 years agoadded the '-tree' parameter to open a tree from the command line
jprocter [Wed, 1 Aug 2007 16:29:14 +0000 (16:29 +0000)]
added the '-tree' parameter to open a tree from the command line

17 years agojavadoc
jprocter [Wed, 1 Aug 2007 16:27:43 +0000 (16:27 +0000)]
javadoc

17 years agoensure current dataset reference is passed to the crossReference search method
jprocter [Wed, 1 Aug 2007 16:27:27 +0000 (16:27 +0000)]
ensure current dataset reference is passed to the crossReference search method

17 years agoadded tree as an applet to application servlet parameter
jprocter [Wed, 1 Aug 2007 16:26:01 +0000 (16:26 +0000)]
added tree as an applet to application servlet parameter

17 years agonull pointer exception bug fix
jprocter [Wed, 1 Aug 2007 16:25:34 +0000 (16:25 +0000)]
null pointer exception bug fix

17 years agodebugging cross references and duplicate sequence db refs
jprocter [Tue, 31 Jul 2007 17:02:48 +0000 (17:02 +0000)]
debugging cross references and duplicate sequence db refs

17 years agotest cc change revoked.
jprocter [Mon, 30 Jul 2007 17:30:21 +0000 (17:30 +0000)]
test cc change revoked.

17 years agotest cc
jprocter [Mon, 30 Jul 2007 17:21:42 +0000 (17:21 +0000)]
test cc

17 years agojavadoc
jprocter [Mon, 30 Jul 2007 17:01:20 +0000 (17:01 +0000)]
javadoc

17 years agoproperty for including debug info in classes
jprocter [Mon, 30 Jul 2007 14:13:53 +0000 (14:13 +0000)]
property for including debug info in classes

17 years agotodo comment
jprocter [Wed, 25 Jul 2007 17:23:28 +0000 (17:23 +0000)]
todo comment

17 years agofix crossRef retrieval so either protein OR nucleotide
jprocter [Wed, 25 Jul 2007 17:17:56 +0000 (17:17 +0000)]
fix crossRef retrieval so either protein OR nucleotide

17 years agouniprot synonym
jprocter [Wed, 25 Jul 2007 17:17:11 +0000 (17:17 +0000)]
uniprot synonym

17 years agobetter vamsas tree io (for when there are no nodemappings)
jprocter [Wed, 25 Jul 2007 17:16:54 +0000 (17:16 +0000)]
better vamsas tree io (for when there are no nodemappings)

17 years agobugfix for vamsas demo
jprocter [Wed, 25 Jul 2007 17:14:23 +0000 (17:14 +0000)]
bugfix for vamsas demo

17 years agoIO rearrangement for AMSAFile output
jprocter [Wed, 25 Jul 2007 17:14:01 +0000 (17:14 +0000)]
IO rearrangement for AMSAFile output

17 years agobugfix for vamsas demo and IO rearrangement for AMSAFile output
jprocter [Wed, 25 Jul 2007 17:13:31 +0000 (17:13 +0000)]
bugfix for vamsas demo and IO rearrangement for AMSAFile output

17 years agoignore random stuff to do with eclipse
jprocter [Fri, 13 Jul 2007 15:40:16 +0000 (15:40 +0000)]
ignore random stuff to do with eclipse

17 years agopreliminary IO classes - read javadoc for purpose
jprocter [Fri, 13 Jul 2007 15:37:21 +0000 (15:37 +0000)]
preliminary IO classes - read javadoc for purpose

17 years agopickmanager on sequence and alignment position, vamsas pick broadcast and refactor...
jprocter [Fri, 13 Jul 2007 15:09:14 +0000 (15:09 +0000)]
pickmanager on sequence and alignment position, vamsas pick broadcast and refactor for new DBRef management and generalised source and entry retrieval mechanism for references and cross references

17 years agorefactor
jprocter [Fri, 13 Jul 2007 15:07:58 +0000 (15:07 +0000)]
refactor

17 years agonew DBRef management and generalised source and entry retrieval mechanism for referen...
jprocter [Fri, 13 Jul 2007 15:07:20 +0000 (15:07 +0000)]
new DBRef management and generalised source and entry retrieval mechanism for references and cross references

17 years agomore semantic groupings of dbs
jprocter [Fri, 13 Jul 2007 15:05:17 +0000 (15:05 +0000)]
more semantic groupings of dbs

17 years agodebugged mappings and translated sequence recovery
jprocter [Fri, 13 Jul 2007 15:04:44 +0000 (15:04 +0000)]
debugged mappings and translated sequence recovery

17 years agopreliminary states for pca distribution io
jprocter [Fri, 13 Jul 2007 15:03:57 +0000 (15:03 +0000)]
preliminary states for pca distribution io

17 years agopreliminary methods for detecting internal sequence nodes
jprocter [Fri, 13 Jul 2007 15:03:32 +0000 (15:03 +0000)]
preliminary methods for detecting internal sequence nodes

17 years agobugfix
jprocter [Fri, 13 Jul 2007 15:02:09 +0000 (15:02 +0000)]
bugfix

17 years agomapping bug fixes
jprocter [Fri, 13 Jul 2007 15:01:48 +0000 (15:01 +0000)]
mapping bug fixes

17 years agobasic idea for recognising that a feature is a coding region.
jprocter [Fri, 13 Jul 2007 15:00:56 +0000 (15:00 +0000)]
basic idea for recognising that a feature is a coding region.

17 years agobugfixes, partially working code for translation using existing translation associate...
jprocter [Fri, 13 Jul 2007 14:59:57 +0000 (14:59 +0000)]
bugfixes, partially working code for translation using existing translation associated with aligned sequences

17 years agocomments for future viz/detection of internal sequence nodes.
jprocter [Fri, 13 Jul 2007 14:58:41 +0000 (14:58 +0000)]
comments for future viz/detection of internal sequence nodes.

17 years agoupdated to iscb demo vamsas-client version
jprocter [Fri, 13 Jul 2007 14:58:12 +0000 (14:58 +0000)]
updated to iscb demo vamsas-client version

17 years agorefactored form of vamsas document interaction code
jprocter [Fri, 13 Jul 2007 14:57:26 +0000 (14:57 +0000)]
refactored form of vamsas document interaction code

17 years agomethods for traversing database reference space
jprocter [Fri, 13 Jul 2007 14:56:27 +0000 (14:56 +0000)]
methods for traversing database reference space

17 years agonew search method for finding references like other references.
jprocter [Fri, 13 Jul 2007 14:55:21 +0000 (14:55 +0000)]
new search method for finding references like other references.

17 years agobugfix and comments
jprocter [Fri, 13 Jul 2007 14:54:55 +0000 (14:54 +0000)]
bugfix and comments

17 years agomoved to castor-1.1-cycle - a specially patched version of castor relating to jira...
jprocter [Fri, 13 Jul 2007 14:54:00 +0000 (14:54 +0000)]
moved to castor-1.1-cycle - a specially patched version of castor relating to jira bugs : jira.codehaus.org/browse/CASTOR-2027 http://jira.codehaus.org/browse/CASTOR-2012 http://jira.codehaus.org/browse/CASTOR-2011

17 years agoensure lines are drawn from first alignment column.
jprocter [Mon, 18 Jun 2007 14:08:57 +0000 (14:08 +0000)]
ensure lines are drawn from first alignment column.

17 years ago1.1 methods
jprocter [Mon, 18 Jun 2007 13:25:26 +0000 (13:25 +0000)]
1.1 methods

17 years agovamsas-client-1.2 schema (mappings and Treenodes) and begun refactoring object bindin...
jprocter [Sun, 17 Jun 2007 13:11:18 +0000 (13:11 +0000)]
vamsas-client-1.2 schema (mappings and Treenodes) and begun refactoring object binding code

17 years agovamsas mouseOvers
jprocter [Sun, 17 Jun 2007 13:08:15 +0000 (13:08 +0000)]
vamsas mouseOvers

17 years agoenable mouseover between DNA coding regions and translated peptide location
jprocter [Sun, 17 Jun 2007 13:06:23 +0000 (13:06 +0000)]
enable mouseover between DNA coding regions and translated peptide location

17 years agoenable mouseover between DNA coding regions and translated peptide location and broad...
jprocter [Sun, 17 Jun 2007 13:04:30 +0000 (13:04 +0000)]
enable mouseover between DNA coding regions and translated peptide location and broadcast to vamsas session.

17 years agofix aligned DNA codon translation bug(s) and generate AlignedCodonFrame mappings...
jprocter [Sun, 17 Jun 2007 13:02:19 +0000 (13:02 +0000)]
fix aligned DNA codon translation bug(s) and generate AlignedCodonFrame mappings for each translated sequence

17 years agorecovery of identical dataset sequence object on undo (rather than creation of a...
jprocter [Sun, 17 Jun 2007 13:01:14 +0000 (13:01 +0000)]
recovery of identical dataset sequence object on undo (rather than creation of a new ds sequence with re-inserted residues)

17 years agoAlignedCodonFrame holds mapping information between individual cDNA regions on dna...
jprocter [Sun, 17 Jun 2007 12:59:15 +0000 (12:59 +0000)]
AlignedCodonFrame holds mapping information between individual cDNA regions on dna and translated peptide sequences

17 years agofix modeller generated PDB file reading bug (missing HEADER line with PDB code)
jprocter [Sun, 17 Jun 2007 12:55:50 +0000 (12:55 +0000)]
fix modeller generated PDB file reading bug (missing HEADER line with PDB code)

17 years agoJnetFIle is a readable format
jprocter [Sun, 17 Jun 2007 12:54:05 +0000 (12:54 +0000)]
JnetFIle is a readable format

17 years agoscore only annotation IO
jprocter [Sun, 17 Jun 2007 12:52:25 +0000 (12:52 +0000)]
score only annotation IO

17 years agomouseOver highlighting and broadcasting efficiency
jprocter [Sun, 17 Jun 2007 12:51:27 +0000 (12:51 +0000)]
mouseOver highlighting and broadcasting efficiency

17 years agothread safety during repaint
jprocter [Sun, 17 Jun 2007 12:47:44 +0000 (12:47 +0000)]
thread safety during repaint

17 years agonull pointer exception fix
jprocter [Sun, 17 Jun 2007 12:46:32 +0000 (12:46 +0000)]
null pointer exception fix

17 years agosearchresult highlighting on common dataset or specific sequenceI residue range
jprocter [Sun, 17 Jun 2007 12:45:25 +0000 (12:45 +0000)]
searchresult highlighting on common dataset or specific sequenceI residue range

17 years agocorrect construction of new dataset sequence when residues are deleted
jprocter [Sun, 17 Jun 2007 12:43:25 +0000 (12:43 +0000)]
correct construction of new dataset sequence when residues are deleted

17 years agojavadoc
jprocter [Sun, 17 Jun 2007 12:41:36 +0000 (12:41 +0000)]
javadoc

17 years agofix for 'RF' annotation tags and ensured parser is robust to new/unknown two letter...
jprocter [Mon, 4 Jun 2007 09:54:31 +0000 (09:54 +0000)]
fix for 'RF' annotation tags and ensured parser is robust to new/unknown two letter annotation tag codes.

17 years agoprototype DBRef and Feature Type semantics (for annotating coding regions and disting...
jprocter [Mon, 28 May 2007 11:15:40 +0000 (11:15 +0000)]
prototype DBRef and Feature Type semantics (for annotating coding regions and distinguishing between DNA and peptide sequence databases)

17 years agomoved castor-mapping.xsd to schemas
jprocter [Mon, 28 May 2007 11:14:05 +0000 (11:14 +0000)]
moved castor-mapping.xsd to schemas

17 years agojalview source development documentation
jprocter [Mon, 28 May 2007 11:12:19 +0000 (11:12 +0000)]
jalview source development documentation

17 years agofix compact annotation array routine
jprocter [Mon, 28 May 2007 10:02:06 +0000 (10:02 +0000)]
fix compact annotation array routine

17 years agocastor mapping file schema (for mappings in resources dir) - this is put in for devel...
jprocter [Mon, 28 May 2007 09:57:21 +0000 (09:57 +0000)]
castor mapping file schema (for mappings in resources dir) - this is put in for development documentation purposes.

17 years agomapping file change for castor-1.1 upgrade
jprocter [Mon, 28 May 2007 09:54:09 +0000 (09:54 +0000)]
mapping file change for castor-1.1 upgrade

17 years agocastor mapping unmarshalling logging
jprocter [Mon, 28 May 2007 09:53:19 +0000 (09:53 +0000)]
castor mapping unmarshalling logging

17 years agologlevel property constants and castor validation logger config
jprocter [Mon, 28 May 2007 09:51:11 +0000 (09:51 +0000)]
loglevel property constants and castor validation logger config

17 years agocastor-1.1 classes (descriptors moved to subpackage)
jprocter [Thu, 24 May 2007 15:20:45 +0000 (15:20 +0000)]
castor-1.1 classes (descriptors moved to subpackage)

17 years agocastor-1.1 compatible classes from ant task
jprocter [Thu, 24 May 2007 15:19:17 +0000 (15:19 +0000)]
castor-1.1 compatible classes from ant task

17 years agojalview 2.0 XML schema versions for backwards compatibility in future castor upgrades
jprocter [Thu, 24 May 2007 15:16:11 +0000 (15:16 +0000)]
jalview 2.0 XML schema versions for backwards compatibility in future castor upgrades

17 years agoNew file for /homes/www-jalview
jprocter [Thu, 24 May 2007 09:08:54 +0000 (09:08 +0000)]
New file for /homes/www-jalview

17 years agofixed jalview 2.3 bug where gapped aligned codons were always translated as inserted...
jprocter [Tue, 22 May 2007 21:17:26 +0000 (21:17 +0000)]
fixed jalview 2.3 bug where gapped aligned codons were always translated as inserted residues rather than aligned with eachother